Azure Dreams-- The evil monster trainer.. (On level 30.)
Final Fantasy 7-- Sephiroth
Final Fantasy 10-- Sir Jecht
(I think the third final boss in the game... the only one that is actually a challenge..)
Metroid II:Return of Samus (Arus)-- The Alien-spacepirate Queen
(This is the harddest boss I've ever fought on ANY game. takes forever to kill.. then you must escape the planet, before it blows up.)
Need for Speed 2: Hot Pursuit-- Not really a boss, but one of the most difficult tracks was the Island Outskirts 2. (The reverse of the first.) It IS my favorite track, and is very difficult.. especially in career mode. You must beat 5 or 6 other Mercedes CLK GTRs and finish first.. I've gotten second. (With 6 laps, if I remember right.) Very hard for a car game.
But the harddest boss I know of from ANY game has to be:
Final Fantasy X: Nemesis
(You have to capture three of every creature, and then beat all creations at the monster arena 10 times each...)
Nemesis has 10,000,000 HP.
Much like Emerald or Ruby from FF7, but much, much harder to beat.